org.brapi.v2.model.geno

Class BrAPIReference

java.lang.Object

org.brapi.v2.model.geno.BrAPIReference

public class BrAPIReference
extends Object

A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable.

Constructor Summary

Constructors

Constructor and Description
BrAPIReference()

Method Summary

Modifier and Type	Method and Description
BrAPIReference	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPIReference	addSourceAccessionsItem(String sourceAccessionsItem)
BrAPIReference	addSourceGermplasmItem(BrAPIReferenceSourceGermplasm sourceGermplasmItem)
BrAPIReference	commonCropName(String commonCropName)
boolean	equals(Object o)
BrAPIReference	externalReferences(List<BrAPIExternalReference> externalReferences)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
String	getCommonCropName() Common name for the crop
@Valid List<BrAPIExternalReference>	getExternalReferences() Get externalReferences
Integer	getLength() The length of this reference's sequence.
String	getMd5checksum() The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).
String	getReferenceDbId() The reference ID.
String	getReferenceName() The unique name of this reference within the Reference Set (e.g.
String	getReferenceSetDbId()
String	getReferenceSetName() The human readable name of a `ReferenceSet`
List<String>	getSourceAccessions() All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g.
Float	getSourceDivergence() The `sourceDivergence` is the fraction of non-indel bases that do not match the reference this message was derived from.
List<BrAPIReferenceSourceGermplasm>	getSourceGermplasm() All known corresponding Germplasm
String	getSourceURI() The URI from which the sequence was obtained.
@Valid BrAPIOntologyTerm	getSpecies() Get species
int	hashCode()
BrAPIReference	isDerived(Boolean isDerived)
Boolean	isIsDerived() A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small.
BrAPIReference	length(Integer length)
BrAPIReference	md5checksum(String md5checksum)
BrAPIReference	putAdditionalInfoItem(String key, Object additionalInfoItem)
BrAPIReference	referenceDbId(String referenceDbId)
BrAPIReference	referenceName(String referenceName)
BrAPIReference	referenceSetName(String referenceSetName)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setCommonCropName(String commonCropName)
void	setExternalReferences(List<BrAPIExternalReference> externalReferences)
void	setIsDerived(Boolean isDerived)
void	setLength(Integer length)
void	setMd5checksum(String md5checksum)
void	setReferenceDbId(String referenceDbId)
void	setReferenceName(String referenceName)
void	setReferenceSetDbId(String referenceSetDbId)
void	setReferenceSetName(String referenceSetName)
void	setSourceAccessions(List<String> sourceAccessions)
void	setSourceDivergence(Float sourceDivergence)
void	setSourceGermplasm(List<BrAPIReferenceSourceGermplasm> sourceGermplasm)
void	setSourceURI(String sourceURI)
void	setSpecies(BrAPIOntologyTerm species)
BrAPIReference	sourceAccessions(List<String> sourceAccessions)
BrAPIReference	sourceDivergence(Float sourceDivergence)
BrAPIReference	sourceGermplasm(List<BrAPIReferenceSourceGermplasm> sourceGermplasm)
BrAPIReference	sourceURI(String sourceURI)
BrAPIReference	species(BrAPIOntologyTerm species)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BrAPIReference

public BrAPIReference()

Method Detail

getReferenceSetDbId

public String getReferenceSetDbId()

setReferenceSetDbId

public void setReferenceSetDbId(String referenceSetDbId)

additionalInfo

public BrAPIReference additionalInfo(com.google.gson.JsonObject additionalInfo)

putAdditionalInfoItem

public BrAPIReference putAdditionalInfoItem(String key,
                                            Object additionalInfoItem)

getAdditionalInfo

public com.google.gson.JsonObject getAdditionalInfo()

Additional arbitrary info

Returns:

additionalInfo

setAdditionalInfo

public void setAdditionalInfo(com.google.gson.JsonObject additionalInfo)

commonCropName

public BrAPIReference commonCropName(String commonCropName)

getCommonCropName

public String getCommonCropName()

Common name for the crop

Returns:

commonCropName

setCommonCropName

public void setCommonCropName(String commonCropName)

externalReferences

public BrAPIReference externalReferences(List<BrAPIExternalReference> externalReferences)

getExternalReferences

@Valid
public @Valid List<BrAPIExternalReference> getExternalReferences()

Get externalReferences

Returns:

externalReferences

setExternalReferences

public void setExternalReferences(List<BrAPIExternalReference> externalReferences)

isDerived

public BrAPIReference isDerived(Boolean isDerived)

isIsDerived

public Boolean isIsDerived()

A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.

Returns:

isDerived

setIsDerived

public void setIsDerived(Boolean isDerived)

length

public BrAPIReference length(Integer length)

getLength

public Integer getLength()

The length of this reference's sequence.

Returns:

length

setLength

public void setLength(Integer length)

md5checksum

public BrAPIReference md5checksum(String md5checksum)

getMd5checksum

public String getMd5checksum()

The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).

Returns:

md5checksum

setMd5checksum

public void setMd5checksum(String md5checksum)

referenceDbId

public BrAPIReference referenceDbId(String referenceDbId)

getReferenceDbId

public String getReferenceDbId()

The reference ID. Unique within the repository.

Returns:

referenceDbId

setReferenceDbId

public void setReferenceDbId(String referenceDbId)

referenceName

public BrAPIReference referenceName(String referenceName)

getReferenceName

public String getReferenceName()

The unique name of this reference within the Reference Set (e.g. '22').

Returns:

referenceName

setReferenceName

public void setReferenceName(String referenceName)

referenceSetName

public BrAPIReference referenceSetName(String referenceSetName)

getReferenceSetName

public String getReferenceSetName()

The human readable name of a `ReferenceSet`

Returns:

referenceSetName

setReferenceSetName

public void setReferenceSetName(String referenceSetName)

sourceAccessions

public BrAPIReference sourceAccessions(List<String> sourceAccessions)

addSourceAccessionsItem

public BrAPIReference addSourceAccessionsItem(String sourceAccessionsItem)

getSourceAccessions

public List<String> getSourceAccessions()

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`.

Returns:

sourceAccessions

setSourceAccessions

public void setSourceAccessions(List<String> sourceAccessions)

sourceDivergence

public BrAPIReference sourceDivergence(Float sourceDivergence)

getSourceDivergence

public Float getSourceDivergence()

The `sourceDivergence` is the fraction of non-indel bases that do not match the reference this message was derived from.

Returns:

sourceDivergence

setSourceDivergence

public void setSourceDivergence(Float sourceDivergence)

sourceGermplasm

public BrAPIReference sourceGermplasm(List<BrAPIReferenceSourceGermplasm> sourceGermplasm)

addSourceGermplasmItem

public BrAPIReference addSourceGermplasmItem(BrAPIReferenceSourceGermplasm sourceGermplasmItem)

getSourceGermplasm

public List<BrAPIReferenceSourceGermplasm> getSourceGermplasm()

All known corresponding Germplasm

Returns:

sourceGermplasm

setSourceGermplasm

public void setSourceGermplasm(List<BrAPIReferenceSourceGermplasm> sourceGermplasm)

sourceURI

public BrAPIReference sourceURI(String sourceURI)

getSourceURI

public String getSourceURI()

The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI.

Returns:

sourceURI

setSourceURI

public void setSourceURI(String sourceURI)

species

public BrAPIReference species(BrAPIOntologyTerm species)

getSpecies

@Valid
public @Valid BrAPIOntologyTerm getSpecies()

Get species

Returns:

species

setSpecies

public void setSpecies(BrAPIOntologyTerm species)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object